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Finding, exploring and filtering frequent sentence-based associations between a disease and a biomedical entity, co-mentioned in disease-related PubMed literature, is a challenge, as the volume of publications increases. Darling is a web application, which utilizes Name Entity Recognition to identify human-related biomedical terms in PubMed articles, mentioned in OMIM, DisGeNET and Human Phenotype Ontology (HPO) disease records, and generates an interactive biomedical entity association network. Nodes in this network represent genes, proteins, chemicals, functions, tissues, diseases, environments and phenotypes. Users can search by identifiers, terms/entities or free text and explore the relevant abstracts in an annotated format. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

ackground: Vertical transmission of Hepatitis B Virus (HBV) is the primary infection source for infants, but little is known on the proportion of children that have acquired HBV from their mothers. Objective: We investigated the relationship of HBV sequencing in HBVpositive children and their mothers and explored the HBV phylogenetic tree. Methods: Serum-extracted HBV-DNA from 38 individuals (13 children paired to nine mothers, 16 unpaired infected children) was amplified by polymerase chain reaction and the target region HBV surface glycoprotein (amino acids 40-171) was directly sequenced. Following editing and alignment of these sequences, phylogenetic tree analysis was performed using the neighbourjoining and maximum-likelihood methods. Results: Analysis was successfully performed in 29 subjects (23 children and six mothers), including six mother-child pairs. All individuals were infected by genotype D. Subgenotype adw3 prevailed (21, 72.4%), followed by ayw2 (4, 13.8%) and ayw3 (4, 13.8%). Among six mother-child pairs, three had identical and three had different subgenotypes. Phylogenetic analysis revealed that HBV sequences from three children did not cluster with their siblings suggesting a different source of infection. Conclusion: Our findings suggest that HBV subgenotypes in infected children may not be identical to their mothers’ and point to non-vertical HBV transmission in childhood.

The provenance of ceramic artefacts is one of the fundamental issues in ceramic analysis and is related to the location a ceramic object was produced or manufactured. This, in turn, refers to the clay source from where the ancient potter exploited their ceramic raw material. Being aware of the local geology is crucial to the identification of potential raw materials for the ceramic manufacturing. Thorough examination of clays in terms of composition, plastic behavior, shrinkage and particle size, is necessary for the evaluation of their suitability for ceramic production. A combination of several analytical techniques can contribute to the iden-tification and characterization of a ceramic raw material. The choice of the proper ones depends on different factors, such as precision, cost, time, expertise, availability and the way a researcher would combine them. The present study aims to unfold the criteria of clay sampling and investigate the appropriateness of the most relevant analytical techniques for the fully characterization of ceramic raw materials and thereafter provenance of ceramics made from them.

The in-depth study of protein–protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present UniReD, a user-friendly, computational prediction tool which analyses biomedical literature in order to extract known protein associations and suggest undocumented ones. As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding a high coverage. We believe that UniReD can become an important and intuitive resource for experimental biologists in their quest for finding novel associations within a protein network and a useful tool to complement experimental approaches (e.g. mass spectrometry) by producing sorted lists of candidate proteins for further experimental validation. UniReD is available at http://bioinformatics.med.uoc.gr/unired/. © The Author(s) 2020. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

International audience; Realistic breast phantoms are often required for supporting the development of microwave and mm-wave imaging systems for breast cancer detection. A number of phantoms have been proposed in the literature, but they are often realized using non-common or toxic materials, and characterized only for the microwave regime. Recently, mm-waves have been also proposed for screening purposes, especially for breast with a high fat content, to provide the resolution vital to detect early-stage cancer masses. Consequently, we proposed several recipes that can be used to create tissue-mimicking materials able to reflect the dielectric properties of different human breast tissues, from fat to neoplastic tissues. In this paper, we present new recipes specifically conceived to mimic up to 50 GHz the dielectric properties of very fat tissues, difficult to achieve otherwise. The involved materials are deionized water, sunflower oil, waste-oil hardener, and two different surfactants (lecithin and Polysorbate 80), all very cheap, easy-to-manage, not-toxic and common materials.

New geological and structural mapping combined with kinematic and amphibole chemistry analyses is used to investigate the deformation history of the Cycladic Blueschist Unit (CBU) on Sifnos Island (Cyclades, Aegean Sea). We concentrate on north Sifnos, an area characterized by exceptionally well-preserved eclogites and blueschists. Our data show that the early, main phase (D2) of ductile deformation in the CBU occurred synchronous with the transition from prograde to close-to-peak retrograde conditions. This deformation phase took place at middle Eocene and is related to ESE-directed thrusting that emplaced the metavolcano-sedimentary subunit over the Marble subunit. The subsequent exhumation-related (D3) deformation is characterized by gently NE-plunging folds and NE-directed contractional shear zones that formed parallel to the axial planes of folds. NE-directed shearing occurred under blue- schist and transitional blueschist-/greenschist-facies conditions during late Eocene–Oligocene and caused the restacking of the early nappe pile. We suggest that a mechanism of ductile extrusion of the CBU in a tectonic setting of net compression could explain better the recorded exhumation-related deformation than a mechanism of syn- and post-orogenic extension. Our new kinematic results in combination with previous works in the Cyclades area reveal a regional scale change in tectonic transport direction from (W)NW–(E)SE at Late Cretaceous–middle Eocene to (E)NE–(W)SW at late Eocene–Oligocene times. The observed change in transport direction may be governed by the relative motion of Africa with respect to Europe during Alpine orogeny.

The aim of this paper is to provide well-stated petrographic reference groups for the recognition of several Sicilian and Spanish Phoenician-Punic production centres in order to facilitate an instrument of further objective support for amphorae provenance. This instrument is based on the crosschecking between data provided by typological studies and the thinsection analysis of amphorae fabrics. It is worth noting that this is only a first step within the framework of a larger research project focused in the creation of an Atlas of Phoenician and Punic Amphorae in the Western Mediterranean including both archaeological and petrographic data. In this context a systematical work on the known production centres characterizing fabrics, pastes and raw materials is the proper way to define workshops and their manufactures and to study their technological choices. Thus we shall give primarily references to well-define workshops as Mozya and Solunto in Sicily and Cadiz and Ebussus in Spain. However, some other petrographic data not obtained from the above cited workshops are also included. In those cases, the reference fabric has to be taken only as a general trend on the petrographic features of a certain large compositional space.

To obtain neurogenic vestibular evoked potentials (NVESTEPs) with surface scalp recording using a tone pip auditory stimulus. Fourteen neurologically normal volunteers (Age range 26-45 years, 10 females and 4 males), and two patients with sensorineural hearing loss and possible multiple sclerosis respectively, were examined. Two channel recordings were obtained, the first channel being P3 referred to Fpz, and the second channel being P4 referred to Fpz. A 1 kHz tone pip stimulus with two cycles was delivered via headphones monoaurally with contralateral masking noise. A consistent negative wave with a mean absolute latency of 4.72 msec was obtained, which we have named N5. 25% of the ears tested had better responses at the ipsilateral parietal electrode. In the patient with bilateral sensorineural hearing loss, NVESTEPs was present, suggesting that the NVESTEP is not a cochlear response. In the patient with possible multiple sclerosis, an abnormal NVESTEP response and a normal BAEP response were found. Use of a tone-pip rather than a click auditory stimulus allows a lower click intensity to be used in the production of NVESTEP responses, leads to a shorter testing time, and is therefore more comfortable for the patient. This study adds to our impression that the NVESTEP may be a physiological response that can be used to assess the vestibular system and is different from the BAEP response. Further testing in patients with symptoms of dizziness and with disorders specific for the vestibular nerve is required.

Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner. Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.

To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function.

Chronic necrotizing pulmonary aspergillosis is a rare infection encountered mainly in immunocompromised patients. We present the case of a young woman where the diagnosis of chronic necrotizing pulmonary aspergillosis was established after an open biopsy of the right lung. Liposomal amphotericin B was administered post-operatively for 10 days with moderate success. In a concise review we summarize the basic notions of chronic necrotizing pulmonary aspergillosis.

International audience

Chemical analysis is a well-established procedure for the provenancing of archaeological ceramics. Various analytical techniques are routinely used and large amounts of data have been accumulated so far in data banks. However, in order to exchange results obtained by different laboratories, the respective analytical procedures need to be tested in terms of their inter-comparability. In this study, the schemes of analysis used in four laboratories that are involved in archaeological pottery studies on a routine basis were compared. The techniques investigated were neutron activation analysis (NAA), X-ray fluorescence analysis (XRF), inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS). For this comparison series of measurements on different geological standard reference materials (SRM) were carried out and the results were statistically evaluated. An attempt was also made towards the establishment of calibration factors between pairs of analytical setups in order to smooth the systematic differences among the results.

To obtain neurogenic vestibular evoked potentials (NVESTEPs) with surface scalp recording using high intensity auditory clicks. The same stimulus is used in myogenic vestibular evoked potentials which has been shown to evoke potentials in the vestibular division of the vestibulocochlear nerve. A whole head recording with surface EEG electrodes was performed using high intensity clicks in one normal volunteer to determine the best recording position for vestibular evoked potentials. The results were compared to responses at moderate click intensities used for brainstem auditory evoked potentials (BAEPs). The difference in the location of the two responses on the scalp was assumed to be from the vestibular system. Responses specific to the high intensity clicks were best obtained in the parietal areas, with no reproducible responses obtained in the same area with moderate intensity clicks normally used in BAEPs. Recordings in neurologically normal volunteers showed a consistent response with a negative polarity at around 3 ms, which we therefore called N3. Two case studies are presented. The first case is a patient with unilateral sensorineural hearing loss with NVESTEPs present, suggesting that NVESTEPs is not a cochlear response. The second case is a patient with multiple sclerosis with demyelinating lesions in the pons and an unobtainable NVESTEP response. NVESTEPs is a possible new diagnostic technique that may be specific for the vestibular pathway. It has potential use in patients with symptoms of dizziness, subclinical symptoms in multiple sclerosis, and in disorders specific for the vestibular nerve.

A selected assortment of Archaic-Hellenistic tableware samples from Solunto, a Phoenician-Punic site located 20 km east of Palermo (Sicily), has been subjected to thin-section petrography and chemical analysis (XRF). In this settlement several ceramic kilns remained operative over a long time period (7th to 3rd century B.C.). The main goal of this analytical study is to distinguish the ceramics manufactured locally from regional and off-island imports. Analytical results were matched to similar data concerning local natural clay sources and to coeval tableware productions from other sites in the same area. The ceramic pastes used by the ancient craftsmen of Solunto in the case of this class of pottery could be differentiated clearly by their petrochemical characteristics. We conclude that ceramics were locally produced far beyond satisfying just internal consumption needs, indicating interaction of Solunto with neighboring Greek colonies, indigenous people, and Phoenician-Punic colonies of Sicily. © 2009 Wiley Periodicals, Inc.

We report the infrared activity, in the spectral region of the OH stretching modes, of different composite silicate glasses whose chemical composition is established by X-ray fluorescence measurements. The analysis of the absorption line profiles is made in terms of different spectral contributions, Gaussian in shape. The comparison with analogous spectra obtained in vitreous silica samples with impurity concentrations < 100 part per million moles is evidence of the effects of the different oxides on the vibrational properties of the OH groups. In particular, for oxide glasses a red shift of the composite band at about 3670 cm(-1), assigned to the OH stretching modes of free Si-OH groups and of water molecules, is found with respect to those silica samples with the smallest impurity concentrations. Moreover, for oxide glasses the absorption activity in the 2500-3200 cm-1 region shows several spectral contributions that depend on the chemical composition of each sample. Also in view of the fact that in this zone no significant absorption activity is revealed in the case of silica samples, these spectral components are assigned to OH stretching modes of Si-OH groups in interaction with the different atoms present (Na, Ca, K, Al, etc.) and/or in modified sites of the vitreous structure.

Petrographic and chemical analyses of the “ceramic body” of 114 majolica artefacts manufactured in Sicily over a wide time range (16th–-19th century) are presented. All the analysed samples, which belong to museums and private collections, were previously attributed to Sicilian workshops based on stylistic features evaluated by expert historians of art. Unambiguous identification of the production sites of majolica handicrafts in Sicily remains, however, open to question when this relies only on purely stylistic considerations. To this end compositional and/or textural markers have been searched for in the “ceramic body” of the majolica artefacts in order to differentiate between the centres of manufacture which were active in Sicily in previous centuries. The study of thin sections has allowed the characterization of the raw materials as well as the microscopic “fabric” of manufacture from four of the more relevant Sicilian production sites, namely: Caltagirone, Sciacca, Palermo and Santo Stefano di Camastra. Chemical data, including minor and trace elements, have been submitted to computer assisted multivariate statistical techniques. Principal component analysis (PCA) and linear discriminant analysis (LDA) have defined compositional “ceramic reference groups” and, consequently, have enabled a more realistic discrimination of provenance. These data have documented several imports of majolica from Naples, while the same artefacts were previously attributed to Sicilian workshops, based on stylistic considerations .